919
(9 years ago)
by duarte:
Fixed bug: was not handling correctly sequences with 'X' in reconstruction
Fixed bug: Pdb.getPhi/Psi were failing because hasCoordinates(int,String) was NullPointing for unobserved residues.
Added test case for getAllPhiPsi

782
(10 years ago)
by duarte:
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.

715
(11 years ago)
by duarte:
New option -s to do split output.
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)

904
(10 years ago)
by duarte:
Moved all decoy scoring stuff to its own package.
Split CombinedScorer into two classes AtomCombinedScorer and ResCombinedScorer. Made combined scorer more efficient: now loading only once the graphs.